Brew fails to install Python: can not symlink - python

I'm trying to install python 2.7 on the latest version of OSX using brew but I get the following error...
.app bundles were installed.
Run `brew linkapps` to symlink these to /Applications.
Warning: Could not link python. Unlinking...
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
You can try again using `brew link python'
Possible conflicting files are:
/usr/local/bin/pip
/usr/local/bin/easy_install-2.7
/usr/local/bin/easy_install
Would anyone know how to fix this error? I tried brew link python but this did not work. I'm new to Linux/OSX, so if this is really obvious, I would still appreciate it if someone could point me in the right direction!

The error means those files already exist in /usr/local/bin
If you 'ls -lF' on that dir, are they sym links that point to a path with the word 'cellar' in it?
If so, then brew already put them in place for you. You're probably missing /usr/local/bin from your PATH
If not, then something else put them there earlier. On a fresh mac, that directory is empty. Brew is a better way to manage those files, so if it was my machine I would remove those files from /usr/local/bin, then you can run brew link. I'd probably keep them in another spot temporarily in case I later discovered a need for them.
Also, run brew doctor when you have a chance. It will tell you about any other problems like this.
Brew wants to own /usr/local/bin. I would let it, it's a great tool.

Fix for macOS Mojave 10.14.2 (2018-12)
I was able to install python with brew using these commands.
brew install python
sudo chown -R $(whoami) $(brew --prefix)/*
sudo install -d -o $(whoami) -g admin /usr/local/Frameworks
brew link python
python3 --version

The most likely answer is that you have somehow installed executables (notably pip and easy-install) that Homebrew packages with it's install of Python outside of the Homebrew workflow. Because Homebrew is not managing these executables (that is, the executables are not symlinks to the versions stored in Homebrew's Cellar repository), its default action is to not overwrite these executables. There are two options you have to resolve this:
You can remove the files that are blocking the installation. Depending on how you installed the executables previously, you might have to do this through manual rm commands. Once you do that, you can run brew link python and Homebrew will happily form the symlinks now that there are no pre-existing executables.
You can tell Homebrew you don't actually care that those executables exist, and you want to overwrite them anyways by using brew link --overwrite python as described in this answer.
In either case, be aware that both pip and easy-install will have dependency files in a site-packages folder somewhere on your computer from their original installation. It would be advisable for you to audit your Python install and your computer for extraneous site-packages folders.

Related

pip fails to find brew installed libs with M1 chip

folks, with new M1 chip brew stores its libraries in the different location /opt/homebrew/ instead of /usr/local/.
And now when pip needs some packages installed by brew(in my case leveldb for plyvel)it's not able to find it until I use Rosetta brew version to put in the old directory: /usr/local/.
I've added eval "$(/opt/homebrew/bin/brew shellenv)" in my .zshrc to import brew-related vars and I thought it should do the thing but no lack.
Do you have any tips on how to handle this issue?
I don't know whether there is a Right Way to do this, but one was is to pass the necessary compiler flags as an environment variable:
CFLAGS="-I/opt/homebrew/include -L/opt/homebrew/lib" python3 -m pip install plyvel
The correct solution to this problem is to include homebrew path in LDFLAGS
export LDFLAGS=-L/opt/homebrew/lib/
and then run the pip command. It is best to add this to your bash / zsh profile (~/.bashrc or ~/.zshrc).

pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available

I am using Python 3.6. When I try to install "modules" using pip3, I face this issue:
pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available
For Windows 10
if you want use pip in normal cmd, not only in Anaconda prompt. you need add 3 environment paths.
like the followings:
D:\Anaconda3
D:\Anaconda3\Scripts
D:\Anaconda3\Library\bin
most people only add D:\Anaconda3\Scripts
MAC OS
I had the same problem on Mac OS(Mojave) and solved the problem as mentioned on this link - Openssl issue.
If you do not have Homebrew or don't know what is Homebrew:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Or if you already have Homebrew installed:
brew update && brew upgrade
brew uninstall --ignore-dependencies openssl; brew install https://github.com/tebelorg/Tump/releases/download/v1.0.0/openssl.rb
Update:
Keep in mind, that I had to use --ignore-dependencies flag, because other packages installed that depend on OpenSSL.
Additional if the problem is caused after using pyenv, you can fix it by using:
brew reinstall python
For Debian users, the following may be of use:
sudo apt install libssl-dev libncurses5-dev libsqlite3-dev libreadline-dev libtk8.6 libgdm-dev libdb4o-cil-dev libpcap-dev
Then cd to the folder with the Python 3.X library source code and run:
./configure
make
make install
I'm using Windows 10 and installed Miniconda 3 with Python 3.7.
I solved this error by following this https://github.com/conda/conda/issues/8273
Specifically, I copied the following files from C:\Users\MyUser\Miniconda3\Library\bin to C:\Users\MyUser\Miniconda3\DLLs:
libcrypto-1_1-x64.dll
libcrypto-1_1-x64.pdb
libssl-1_1-x64.dll
libssl-1_1-x64.pdb
For centos 7:
Install openssl:
sudo yum install openssl-devel
now goto python directory were we extracted the python tar,
run below commands
sudo ./configure
sudo make
sudo make install
This will fix the problem in centos...
For future Oracle Linux users trying to solve this, below is what worked for me.
First install missing libs:
yum install zlib-devel bzip2-devel openssl-devel ncurses-devel sqlite-devel
readline-devel tk-devel gdbm-devel db4-devel libpcap-devel xz-devel
Then cd to your Python3.X library and run:
make
make install
macOS, pyenv
In case of your python being an pyenv installed one, where pyenv is installed with homebrew on macOS, there might me a newer version available which fixes this:
$ brew update && brew upgrade pyenv
Then reinstalling the python version:
$ pyenv install 3.7.2
pyenv: /Users/luckydonald/.pyenv/versions/3.7.2 already exists
continue with installation? (y/N)
Note, it is a bit dirty to overwrite the existing python install like that, but in my case it did work out. Probably cleaner to delete it and then recreate it properly.
For Windows 10,windows 7
If pip install is not working on CMD prompt, run it using Anaconda prompt - it works.
https://github.com/pypa/virtualenv/issues/1139
Worked for me.
sudo apt-get install libssl-dev
Use this to enable ssl for pip.
Let me know if someone encounters issues.
Encountered this issue while installing python 3.8 from source on ubuntu. The steps needed to install it successfully alongside the default python 3.7 are summarised below :
sudo apt -y install libssl-dev zlib1g-dev build-essential
wget https://www.python.org/ftp/python/3.8.0/Python-3.8.0.tgz
tar -xf Python-3.8.0.tgz
cd Python-3.8.0/
./configure --enable-optimizations
make
sudo make altinstall
The install instruction for zlib1g-dev and build-essential is redundant, as ubuntu desktop already has these, but was necessary for some of Amazon's EC2 instances. python 3.8.0 is the current release just now, but should be replaced with the latest available.
These instructions are best for keeping python 3.7 as the default for python3, and running python 3.8 in a virtual environment.
Similar to the above solution reinstall the python version with pyenv.
Somehow, I upgraded my openssl which broke the pyenv version python.
pyenv install 3.6.8
python-build: use openssl#1.1 from homebrew
python-build: use readline from homebrew
...
The first line says it relies on the homebrew openssl.
In my case, I reinstalled Python. It solved the problem.
brew reinstall python
For OpenSUSE in the same manner, but a few changes of listed above packages:
zypper install zlib-devel libopenssl-devel ncurses-devel sqlite3-devel readline-devel tk-devel gdbm-devel libpcap-devel xz-devel
Then cd to Python sources dir and
make
make install
or
make
make altinstall
And perhaps
ln -s /usr/local/lib64/python3.6/lib-dynload/ /usr/local/lib/python3.6/lib-dynload
should be executed for OpenSUSE users. See Python 3.7 install not working on openSUSE Leap 42.3
Just try installing through Anaconda prompt
I ran into this issue with Visual Studio Code installing pylint from the VS Code prompt.
I was able to overcome the issue by opening the Anaconda installation directory and running
pip install pylint
Then VS Code was happy, but that did not fix the issue as running
& C:/Users/happy/Anaconda3/python.exe -m pip install -U pylint
pretty much gave the same error so it seems that VS Code is unable to access the python modules.
Note that VS Code picks up the first python env it see when installed, the bottom left of the screen indicates which env is being used. Clicking on that area allows to set the environment. So even if you ran the pip install for an environment VS Code could be looking at a different one.
Best approach was to make sure that VS code had the correct python environment selected and that same environment is in the system PATH (under System Properties --> Advanced --> Environmental Variables)
Under the Path Variable, Edit and browse to the specific Anaconda directory that you want VSCode to use and add to PATH, I needed to Add the following:
C:\Users\happy\Anaconda3\
C:\Users\happy\Anaconda3\Scripts\
C:\Users\happy\Anaconda3\Library\bin\
C:\Users\happy\Anaconda3\Library\mingw-w64\bin\
Your Anaconda installation directory may differ.
One note is that Windows does not have the PATH variable take effect until you restart the terminal. In this case close and re-op VS code. If using a Terminal or PS Shell then close and reopen and check Path to make sure it is included.
The problem probably comes from your installed openssl package version. That was the case for me and I fixed this issue just upgrading it. I'm on Mac OS, using brew :
brew upgrade openssl
If you installed python with brew, this should directly fix the issue with it, as python is dependent on openssl
Newest Python 3.8.4 or higher should able to support https protocol out of box. If you still have old python installation on your pc - either download & install python3 manually, or using Chocolatey:
If you don't have Chocolatey, install it - from here: https://chocolatey.org/docs/installation
You can just copy paste one command line liner and execute it from command prompt with elevated priviledges.
choco install python3
if you don't have python3 installed, or you you have it installed - then:
choco upgrade python3
Notice also that you can use also anaconda distribution, as it has built-in python with https support, but this rather ancient instructions, no need to follow them anymore.
Install anaconda, using command line:
choco install anaconda3
Set environment variables:
set PATH=C:\tools\Anaconda3\Scripts;C:\tools\Anaconda3;C:\tools\Anaconda3\Library\bin;%PATH%
and then run command which failed. In my case it was:
pip install conan
Anaconda uses separate python installation, and pip is also anaconda specific.
As Tokci said, it also works for Windows 7.
"Go with the mouse to the Windows Icon (lower left) and start typing "Anaconda". There should show up some matching entries. Select "Anaconda Prompt". A new command window, named "Anaconda Prompt" will open."
Then pip works.
The following also helped to import xgboost:
https://www.youtube.com/watch?v=05djBSOs1FA
If someone is using Arch Linux OS, I solved the TLS/SSL problem by running this:
sudo pacman -S openssl
Then I could use pip to install the package I needed:
pip install openpyxl
Go to Anaconda prompt and type (if you have python 3.x installed on your engine) :
py -m pip install pymysql
i was having the same issue and this solved my problem. later after doing this you can import pymysql in power shell or any other prompt.
The issue is due to OpenSSL package is missing on your PC.
If pip install openpyxl also gives error.
you can fix this by installing OpenSSL(Win64 OpenSSL v1.1.1g) from below site :
slproweb.com/products/Win32OpenSSL.html
Restart the IDE you are using, for changes to be in effect.
In Windows 10 SQL Server 19 the solution is known.
Copy the following files:
libssl-1_1-x64.dll
libcrypto-1_1-x64.dll
from the folder
C:\Program Files\Microsoft SQL Server\MSSSQL15.MSSQLSERVER\PYTHON_SERVICES\Library\bin
to the folder
C:\Program Files\Microsoft SQL Server\MSSSQL15.MSSQLSERVER\PYTHON_SERVICES\DLLs
Then open a new DOS command shell prompt.
From https://learn.microsoft.com/en-us/sql/machine-learning/troubleshooting/known-issues-for-sql-server-machine-learning-services?view=sql-server-ver15#7-unable-to-install-python-packages-using-pip-after-installing-sql-server-2019-on-windows
Worked for me.
pkg install openssl
Use this to enable ssl.
Currently there is same issue in Anaconda prompt (Anaconda3) on Windows 10. Here is workaround: https://github.com/ContinuumIO/anaconda-issues/issues/10576
Fixed this without having to change anything related to TSL/SSL.
I was trying to see if the same thing was happening to pip, and saw that pip was broken. Did some digging and realized it's probably caused by Homebrew deleted python#2 on February 1st, 2020.
Running brew uninstall python#2 to delete python2 installed by Homebrew.
Destroyed the virtual env created using python3 and created a new one. pip3 installing works fine again.
I am on macOS and I had used brew but what Vaulstein mentioned in his answer didn't cover my case.
I run the following commands to make sure my current python was not installed by brew
brew list | grep python
python
python#2
brew info python
python#3.8: stable 3.8.3 (bottled)
Interpreted, interactive, object-oriented programming language
https://www.python.org/
Not installed
...
So I download the latest 3.8.5 from https://www.python.org/ and when installing it I saw following information
Certificate verification and OpenSSL
This package includes its own private copy of OpenSSL 1.1.1. The
trust certificates in system and user keychains managed by the
Keychain Access application and the security command line utility are not used as defaults by the Python ssl module
After installed 3.8.5 it fixed the problem.
I got into this problem using Ubuntu, pyenv and Python 3.8.1 managed by pyenv. There was actually no way to get pip to work correctly, since every time I tried to install anything, including pip itself, the same error showed up.
Final solution was to install, via pyenv, a newer version, in this case 3.8.6. Apparently, from 3.8.4 Python is prepared to run SSL/TLS out of the box, so everything worked fine.
I simply solved the problem with following command:
brew upgrade python#3.9
SSL is included by default on this version!
In my case I was running into issues with my $PATH on Linux. This can also happen on MacOS.
Check to see if /usr/bin/pip3 install package_name_goes_here works for you. If so then run
which pip3 this will tell you which is the first directory that pip3 is installed in.
If it is something like /usr/local/bin/pip3 which is different from /usr/bin/pip3 then you may need to adjust your $PATH.
Run
echo $PATH and copy the result.
The PATH is simply a colon separated list of directories that contain directories. Bash will always return the first instance of the program that you are attempting to execute. Move all the system directories upfront. Here is a list of some of the system directories:
/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
If that fails then verify you have openssl installed by running openssl version -a if not then install openssl.
If you've installed anaconda via scoop, and encounter this error while using pip from within a conda environment you can resolve it by...
Adding these to your path
C:\Users\YOUR_USERNAME\scoop\apps\anaconda3\current
C:\Users\YOUR_USERNAME\scoop\apps\anaconda3\current\Scripts
C:\Users\YOUR_USERNAME\scoop\apps\anaconda3\current\Library
C:\Users\YOUR_USERNAME\scoop\apps\anaconda3\current\Library\bin
Installing openssl via scoop
scoop install openssl
And copying the following DLLs from ..\anaconda3\Library\bin to ..\anaconda3\DLLs
References:
https://stackoverflow.com/a/54897379
https://stackoverflow.com/a/60405693

Python not finding pip modules MacOS

I have installed some modules using pip and whenever I try to import them in Python I am told that no module exists. I think there is something wrong with my paths. This is some terminal output, does anyone know how I can fix this?
Nicks-MacBook-Pro:~ nickporter$ which python
/usr/bin/python
Nicks-MacBook-Pro:~ nickporter$ which pip
/usr/local/bin/pip
Nicks-MacBook-Pro:~ nickporter$
You can use pip freeze to find the packages installed.
I do not know whether you use a virtualenv. If you use it, you have to source it, to activate it.
It looks like you probably have multiple installations of Python or pip (or both). First, determine if you have multiple Python binaries installed and decide on the one you want to use by default.
You clearly have /usr/bin/python...check if there is another one in /usr/local/bin/python. If you do have one in /usr/local/bin, I'm guessing you installed it with Homebrew. Pick the Python you want to use (if there are multiple) by playing with your PATH. If you want to use /usr/local/bin/python (assuming it exists) ensure /usr/local/bin comes before /usr/bin in your PATH.
Once you do that, I would remove your current pip. After you remove it, look for it again with which pip, just to make sure you don't have any old one laying around. Once you've totally removed it, reinstall.
If you're installing with Homebrew, I'd stick to using the Homebrew python and pip. If you're not using Homebrew I'd install pip using: https://bootstrap.pypa.io/get-pip.py
curl -q https://bootstrap.pypa.io/get-pip.py | sudo python
You have homebrew version of python shadowed by the system python, but because system python doesn't have pip, a pip you see is actually a brew one.
I found, that the reason for this is that brew by default names python2.7 as python2 in /usr/local/bin (probably for preventing possible compatibility issues with some system services (?)) , i.e. you may try to run python2 or try to ln /usr/local/bin/python2 /usr/local/bin/python and restart the term session.
Make sure that /usr/local/bin goes before /usr/bin and /bin in your $PATH.
BTW. brew info {package} often contains recommendations for proper configuration of packages.

"Bad" Python Install

I've been having issues with Python recently, such as compatibility with anaconda. When I ran Homebrew's brew doctor, I think I came across the problem, as laid out below. How can I wipe these files and do a clean install of Python?
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
/Library/Frameworks/Python.framework/Versions/3.4/bin/python3-config
/Library/Frameworks/Python.framework/Versions/3.4/bin/python3.4-config
/Library/Frameworks/Python.framework/Versions/3.4/bin/python3.4m-config
/opt/local/bin/curl-config
/opt/local/bin/freetype-config
/opt/local/bin/libpng-config
/opt/local/bin/libpng16-config
/opt/local/bin/nc-config
/opt/local/bin/ncurses5-config
/opt/local/bin/ncursesw5-config
/opt/local/bin/pcre-config
/opt/local/bin/python2.7-config
/opt/local/bin/xml2-config
/Users/adamg/anaconda/bin/freetype-config
/Users/adamg/anaconda/bin/libdynd-config
/Users/adamg/anaconda/bin/libpng-config
/Users/adamg/anaconda/bin/libpng15-config
/Users/adamg/anaconda/bin/llvm-config
/Users/adamg/anaconda/bin/nc-config
/Users/adamg/anaconda/bin/python-config
/Users/adamg/anaconda/bin/python2-config
/Users/adamg/anaconda/bin/python2.7-config
/Users/adamg/anaconda/bin/xml2-config
/Users/adamg/anaconda/bin/xslt-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7-config
Warning: Python is installed at /Library/Frameworks/Python.framework
Homebrew only supports building against the System-provided Python or a
brewed Python. In particular, Pythons installed to /Library can interfere
with other software installs.
To uninstall using brew use this command brew uninstall <package>.
Mac OS X has python preinstalled so there is no need to install another Python instance unless it's necessary.
You can run brew install python to install Python using Homebrew.
Even though python is preinstalled as #jgritty hinted in comments, you may consider not to rely on it for development purposes.
So you should brew uninstall python then brew install python.
In order to remove an installed Python (2.7) instance, you need to run the following commands in your terminal;
sudo rm -rf /Library/Frameworks/Python.framework/Versions/2.7
sudo rm -rf "/Applications/Python 2.7"
remove the symbolic links in /usr/local/bin that point to this python version see ls -l /usr/local/bin | grep '../Library/Frameworks/Python.framework/Versions/2.7'
if necessary, edit your shell profile file(s) to remove adding /Library/Frameworks/Python.framework/Versions/2.7 to your PATH environment file. Depending on which shell you use, any of the following files may have been modified: ~/bash_login, ~/bash_profile, ~/cshrc, ~/profile, ~/tcshrc, and/or ~/zprofile.
A reference by #Ned Deily available at this link.
You can do brew list to see what brew has installed.
If python and python3 are not in that list, you may want to install either or both.
Based on these files:
/Library/Frameworks/Python.framework/Versions/3.4/bin/python3-config
/Library/Frameworks/Python.framework/Versions/3.4/bin/python3.4-config
/Library/Frameworks/Python.framework/Versions/3.4/bin/python3.4m-config
I would guess you ran a python 3.4 install downloaded directly from python.org or somewhere else.

Python audiolab install, unable to install (or find) libsndfile on Mac OSX

Trying to install scikits.audiolab-0.11.0 on Mac, bit it requires libsndfile: http://www.mega-nerd.com/libsndfile/. I did install libsndfile supposedly, using libsndfile_python-1.0.0-py2.7-macosx10.5.mpkg, but the audiolab setup gives an error: libsndfile library not found. The error from the audiolab installer is below. It suggests that the location of the libsndfile can be specified in the site.cfg.
My inexperience with these type of installs are getting in the way of understanding this. Can anyone offer some advice on how to get this done?, or answer my questions below?
If the libsndfile was installed, where would it be, so I can specify the location? Else how to install it properly?
What is the site.cfg file? I see a site.cfg.bdist_wininst, and a site.cfg.win32 in the scikits.audiolab-0.11.0 folder that I downloaded.
What is meant by "specified in the site.cfg file in section [sndfile]" (see error below). Does this mean that I should replace the word "sndfile" with the /path/to/libsndfile between the brackets?
By the way, I checked in my /usr/lib dir and there is no libsndfile. I take it that there is where the audiolab setup will look for the file, by default.
Thanks for reading, and any help.
Error from audiolab installer:
numpy.distutils.system_info.NotFoundError: sndfile (http://www.mega-nerd.com/libsndfile/) library not found.
Directories to search for the libraries can be specified in the
site.cfg file, in section [sndfile].
libsndfile_python sounds like a binding to libsndfile rather than libsndfile itself. You probably do not have libsndfile installed. It should, however, be quite easy to install if you already have the developer tools installed:
First, download the latest source.
Unpack it somewhere.
Open Terminal and cd to the directory you unpacked.
Configure it: ./configure
Build it: make -j8
Install it (requires administrative rights): sudo make -j8 install
You can then delete the directory you unpacked, but you may want to keep it for easy uninstallation.
To install libdsnd in a mac (Tested in a Yosemite 10.10.3):
1- Install Homebrew (paste this on a terminal):
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
2- Install libsnd:
brew install libsndfile
3- Link libsnd:
brew link --overwrite libsndfile
4- Install scikits.audiolab:
sudo easy_install scikits.audiolab
There you go!
For windows users:
Download file :
"scikits.audiolab‑0.11.0‑cp27‑cp27m‑win32.whl"
from "https://www.lfd.uci.edu/~gohlke/pythonlibs/#scikits.audiolab"
Install it using command : pip install scikits.audiolab‑0.11.0‑cp27‑cp27m‑win32.whl
install libsndfile from http://www.mega-nerd.com/libsndfile/ using setup:
http://www.mega-nerd.com/libsndfile/files/libsndfile-1.0.28-w32-setup.exe
copy "libsndfile-1.dll" from C:\Program Files (x86)\Mega-Nerd\libsndfile\bin
to folder Lib\site-packages\scikits\audiolab folder within your Python installation folder,
ex: C:\Python2711\Lib\site-packages\scikits\audiolab
For me this solved a problem.
Credits to "https://github.com/cournape/audiolab/issues/7" - "samuelgarcia"

Categories